def passthrough(args):
"""
%prog passthrough chrY.vcf chrY.new.vcf
Pass through Y and MT vcf.
"""
p = OptionParser(passthrough.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
vcffile, newvcffile = args
fp = open(vcffile)
fw = open(newvcffile, "w")
gg = ["0/0", "0/1", "1/1"]
for row in fp:
if row[0] == "#":
print(row.strip(), file=fw)
continue
v = VcfLine(row)
v.filter = "PASS"
v.format = "GT:GP"
probs = [0] * 3
probs[gg.index(v.genotype)] = 1
v.genotype = v.genotype.replace("/", "|") + \
":{0}".format(",".join("{0:.3f}".format(x) for x in probs))
print(v, file=fw)
fw.close()
def validate(args):
"""
%prog validate imputed.vcf withheld.vcf
Validate imputation against withheld variants.
"""
p = OptionParser(validate.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
imputed, withheld = args
register = {}
fp = open(withheld)
for row in fp:
if row[0] == "#":
continue
v = VcfLine(row)
register[(v.seqid, v.pos)] = v.genotype
logging.debug("Imported {0} records from `{1}`".\
format(len(register), withheld))
fp = must_open(imputed)
hit = concordant = 0
seen = set()
for row in fp:
if row[0] == "#":
continue
v = VcfLine(row)
chr, pos, genotype = v.seqid, v.pos, v.genotype
if (chr, pos) in seen:
continue
seen.add((chr, pos))
if (chr, pos) not in register:
continue
truth = register[(chr, pos)]
imputed = genotype.split(":")[0]
if "|" in imputed:
imputed = "/".join(sorted(genotype.split(":")[0].split("|")))
#probs = [float(x) for x in genotype.split(":")[-1].split(",")]
#imputed = max(zip(probs, ["0/0", "0/1", "1/1"]))[-1]
hit += 1
if truth == imputed:
concordant += 1
else:
print(row.strip(), "truth={0}".format(truth), file=sys.stderr)
logging.debug("Total concordant: {0}".\
format(percentage(concordant, hit)))
def mitocompile(args):
"""
%prog mitcompile *.vcf.gz
Extract information about deletions in vcf file.
"""
from jcvi.formats.vcf import VcfLine
from six.moves.urllib.parse import parse_qsl
p = OptionParser(mitocompile.__doc__)
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
vcfs = args
print("\t".join("vcf samplekey depth seqid pos alt svlen pe sr".split()))
for i, vcf in enumerate(vcfs):
if (i + 1) % 100 == 0:
logging.debug("Process `{}` [{}]".format(vcf, percentage(i + 1, len(vcfs))))
depthfile = vcf.replace(".sv.vcf.gz", ".depth")
fp = must_open(depthfile)
chrm, depth = fp.next().split()
depth = int(float(depth))
samplekey = op.basename(vcf).split("_")[0]
fp = must_open(vcf)
for row in fp:
if row[0] == "#":
continue
v = VcfLine(row)
info = dict(parse_qsl(v.info))
print(
"\t".join(
str(x)
for x in (
vcf,
samplekey,
depth,
v.seqid,
v.pos,
v.alt,
info.get("SVLEN"),
info["PE"],
info["SR"],
)
)
)